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Seattle transportation director Scott Kubly is under a city ethics investigation related to the struggling Pronto bike-share system.

The investigation comes as the City Council voted 7-2 this month to spend $1.4 million to buy the bike-share program, which started Seattle operations Oct. 13, 2014. In addition, the city paid Pronto $305,000 over the winter, without notifying the council first, to help the money-losing nonprofit continue service.

The 500 green bikes averaged less than one user each per day during Pronto’s first year, the data show.

Kubly confirmed the investigation by phone Tuesday. “I’m going to cooperate fully with it,” he said.

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“I understand an ethics complaint has been filed about the bike-share program,” Kubly said in a statement Tuesday evening. “The Seattle Ethics and Elections Commission exists to investigate such complaints. To ensure the investigation is comprehensive and maintains its full integrity, I will wait until the investigation is complete to provide comment on it.”

Kubly declined to elaborate about the nature of the ethics complaint or who filed it.

Officials with the Seattle Ethics and Elections Commission couldn’t be reached for comment Tuesday evening.

The investigation’s existence was first reported by KING 5, which said the city is paying $20,000 for an independent inquiry by Marilyn Brenneman, a former prosecutor.

Ref Lindmark, chairman of the Pronto board, said he hasn’t been contacted in the investigation. Holly Houser, former Pronto executive director, didn’t immediately respond to a call seeking comment.

In approving the buyout, the City Council passed an amendment saying Mayor Ed Murray and the council will choose a future operating company if the bike-share system expands, rather than Kubly making the selection.

Councilmembers Tim Burgess and Lisa Herbold voted against the purchase.

When he was hired as transportation director in mid-2014, he left his position as president of Alta Bike Share, which was hired earlier that year to run Pronto in Seattle. Alta has since been bought by New York-based Motivate, a leading operator of bike-share systems in many cities.

Previously, Kubly held senior positions at transportation departments in Chicago and Washington, D.C., which also contracted with Alta for its bike systems.

Kubly is not a board member or executive at Motivate. He has said in interviews he has no financial ties to the company.

“Scott’s past, there was never anything hidden. Everything I heard was out in the open,” said Lindmark, who also worked on last year’s winning $930 million city transportation-levy campaign.